CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination
CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination
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DOI：
10.1186/s12859-020-03619-x
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发表时间：
2020-06-24
影响因子：
3
通讯作者：
Bobay, Louis-Marie
中科院分区：
文献类型：
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作者：
Bobay, Louis-Marie
背景原核生物是无性的，但这些生物经常进行同源重组，这一过程不同于有性生物的减数分裂重组。大多数用于模拟基因组进化的工具要么假设有性生殖，要么假设种群中完全没有DNA通量。因此，很少有模拟器适用于模拟原核基因组进化，同时考虑重组。此外，许多模拟器都是基于聚结的，它假设了一个中性的基因组进化模型，这些模拟器最适合在弱选择压力下进化的生物体，如动物和植物。相比之下，原核生物被认为是在更强的选择压力下进化的，这表明时间向前的模拟器更适合这些生物。结果在这里，我介绍了CoreSimul，一个用于原核生物同源重组建模的核心基因组进化的实时模拟器。模拟由系统发育树指导，并结合不同的取代模型，包括密码子选择模型。结论CoreSimulis是一个灵活的向前的时间模拟器，构成了一个重要的除了有限的列表可用的模拟器适用于原核生物基因组进化。
Background Prokaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms. Most tools developed to simulate genome evolution either assume sexual reproduction or the complete absence of DNA flux in the population. As a result, very few simulators are adapted to model prokaryotic genome evolution while accounting for recombination. Moreover, many simulators are based on the coalescent, which assumes a neutral model of genomic evolution, and those are best suited for organisms evolving under weak selective pressures, such as animals and plants. In contrast, prokaryotes are thought to be evolving under much stronger selective pressures, suggesting that forward-in-time simulators are better suited for these organisms. Results Here, I presentCoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection. Conclusions CoreSimulis a flexible forward-in-time simulator that constitutes a significant addition to the limited list of available simulators applicable to prokaryote genome evolution.